OK, lets see.
Remember when Elliot was dating Paul, the male nurse? She was uncomfortable with the relationship initially because she felt she couldn't date a man in a lower position than her. Thus reinforcing the belief that the man should be in at least an equal position to the woman, preferably superior.
Elliot's portrayal switched between a little girl, lost, who needed protecting from the big, scary world, and being someone who didn't pay much attention to whose feelings she was trampling over.
Carla had been stuck in the position of "nurse" for nine years. It wasn't until Turk came along that she was able to enrol on a training course so she could administer medicines, and give her more authority in the hospital. Because us women need men to finance us if we are going to improve...
Kim lied about having miscarried or aborted JD's baby. Seeing as us women are cold and callous like that.
In the episode where Kelso demands Elliot removes her make up and starts acting proffessional, the janitor tells Kelso that he enjoys seeing Elliot like that (make up, etc...). Seeing as, y'know, she's not there to do anything important like save lives... Just provide eye candy for the male members of staff.
Cox frequently belittles JD by calling him girls names. Because, y'know. That's the worst insult you can give a man. Compare him to a female. 
And the Janitor's wedding episode has been pointed out.
All of the characters (except The Todd) were consistently in relationships, reaffirming the idea that you can only be truly happy when in love, and singledom makes you miserable and lonely, etc...
A few things the show did get right, though.
Most of the regular female characters were portrayed as strong, independent women.
Elliot was shown as being JD's equal through most of the series. They even got promoted at the same time, if I remember correctly, with Elliot getting the majority of the power?
I also felt "Cookie Pants" was quite an important episode. Elliot was willing to let JD see her in her "cookie pants" and sans make up (I think), something she felt was unattractive, and he said something along the lines of how she looked even more beautiful than ever... Not hunting the episode out this time of night, but I'll double check...
We also saw quite a bit of Cox, JD and Turk caring for their DC, while their wives/partners carried on their careers. This, to me, reaffirmed the message that children were equal responsibility between two responsible parents, and promoted the idea of men caring for DC as being a good thing.
I may have to rewatch the box set, in my cookie pants, with a tub of Ben and Jerry's. All in the name of research, y'know? 